PHILADELPHIA — Zack Wheeler was so good this season, the Mets ended his early.

Manager Mickey Callaway announced Wednesday that Wheeler has been shut down two starts early because of workload concerns — 100 more innings this season than he pitched in 2015-17 combined — not any health issues. Corey Oswalt will take Wheeler’s place in the rotation, including Saturday against the Nationals.

After 29 starts, plus one in Triple-A Las Vegas to open the year, Wheeler finished with career-best marks in ERA (3.31), WHIP (1.12), FIP (3.24), strikeouts per walk (3.25) and innings (187 1/3).

“We’re really excited about the year he had,” Callaway said. “And we feel like we’d probably be taking the best care of him we can if we shut him down at this point.”

Said Wheeler: “I feel like I had a good season. I would have liked to finish it out, but getting [about] 100 more innings than last season, not doing all that much the past two and a half years, it makes some sense to get ahead and shut it down and not really push it.”

Wheeler pitched himself out of the rotation in spring training, which led to the brief minor-league stint, but quickly returned to the majors and made as large a leap as any Mets pitcher under first-year manager Callaway and new pitching coach Dave Eiland.

With a refined delivery and an improved between-starts routine, Wheeler threw harder than ever (96.6 mph on his fastball), added a new pitch (a splitter) and really rounded into form in the second half, going at least seven innings in 12 of his last 16 starts. He lowered his ERA at the start of June (5.40) by more than two points.

Wheeler’s 1.68 ERA in the second half is fourth-best in the majors, edging Jacob deGrom (1.94).

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“This stretch that he had has really kind of opened his eyes,” Callaway said. “He always knew he could be this guy, but when you’re actually that guy, it kind of opens your eyes to, ‘OK, I’ve got this, I’m going to move forward with it.’ Hopefully this is a big stepping stone for him in his career.”

As much as anything else, finally being healthy was critical for Wheeler, who made only 17 starts the previous three seasons because of various injuries. He said Wednesday he feels healthy aside from the wear and tear typical of this time of year.

“If I really needed to, like if we were in the playoff push or something, I could definitely go out there and finish it up,” Wheeler said. “That’s not why I’m stopping. It’s being smart, really.”

Flores back to NYC

Wilmer Flores returned to New York City on Wednesday to get his knees checked out Thursday. He could be available as soon as Thursday night when the Mets visit the Nationals, Callaway said.

The origin of the knee pain is unknown. Callaway said both of Flores’ knees hurt. Flores said his right knee has been bothering him for two months, and his left knee hasn’t been bothering him. He’ll get tests on both.

“I’m getting the other one checked out, but it’s not bothering me,” Flores said. “Why not?”

Flores said he didn’t tell the team he was having trouble “because I wanted to keep playing.” But he has started only two of the Mets’ past 13 games through Wednesday.

“Since I wasn’t out there every day, if the doctor says I really need to rest, I’ll just rest,” Flores said. “Hopefully there’s nothing bad there.”